Here's one idea I've had:
Take your other favourite major sport, and play out its league history in MLB's place. In my case I was thinking of following the NHL's history in terms of league sizes and cities, expansions, alignments, etc., only the teams would play baseball instead of hockey.
This way you have your cities, alignments, and expanions already laid out for you, but you get to create new history with the baseball scores. You do have to make some changes (i.e. you can't really duplicate the 21 team NHL years for example) but overall you can follow this other league's history but with them playing baseball instead of the original sport.